5QU9 | pdb_00005qu9

PanDDA analysis group deposition of ground-state model of Kalirin/Rac1 screened against a customized urea fragment library by X-ray Crystallography at the XChem facility of Diamond Light Source beamline I04-1

• PDB DOI: https://doi.org/10.2210/pdb5QU9/pdb
• Deposition Group: G_1002111 (ground state) ExploreG_1002111

• Classification: HYDROLASE/TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-12-13 Released: 2020-01-29 
• Deposition Author(s): Gray, J.L., Krojer, T., Talon, R., Douangamath, A., Jimenez Antunez, C., Bountra, C., Arrowsmith, C.H., Edwards, A., Brennan, P.E., von Delft, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.231 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Literature

PanDDA analysis group deposition of ground-state model

Gray, J.L., Krojer, T., Talon, R., Douangamath, A., Jimenez Antunez, C., Bountra, C., Arrowsmith, C.H., Edwards, A., Brennan, P.E., von Delft, F.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 41.13 kDa 
• Atom Count: 3,118 
• Modelled Residue Count: 356 
• Deposited Residue Count: 360 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related C3 botulinum toxin substrate 1	A	178	Homo sapiens	Mutation(s): 0  Gene Names: RAC1, TC25, MIG5 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P63000 (Homo sapiens) Explore P63000  Go to UniProtKB:  P63000
PHAROS:  P63000 GTEx:  ENSG00000136238

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Kalirin	B	182	Homo sapiens	Mutation(s): 0  Gene Names: KALRN, DUET, DUO, HAPIP, TRAD EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O60229 (Homo sapiens) Explore O60229  Go to UniProtKB:  O60229
PHAROS:  O60229 GTEx:  ENSG00000160145

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.231 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.517	α = 90
b = 63.517	β = 90
c = 345.928	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-01-29 
Deposition Author(s): Gray, J.L., Krojer, T., Talon, R., Douangamath, A., Jimenez Antunez, C., Bountra, C., Arrowsmith, C.H., Edwards, A., Brennan, P.E., von Delft, F.

Revision History  

• Version 1.0: 2020-01-29
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references